Research workbench
Human cytomegalovirus terminase nuclease domain, mn soaked, inhibitor bound
Analyse Human cytomegalovirus terminase nuclease domain, mn soaked, inhibitor bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EY7
- Type
- protein
- Length
- 887 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- UL89 hcmv terminase
- UniProt
- P16732
- Ligands
- C3W, MN, CL
- Pockets
- 8 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 41% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | UL89 hcmv terminase | protein | 225 | 42% helix, 25% strand | P16732 |
| B | UL89 hcmv terminase | protein | 227 | 40% helix, 25% strand | P16732 |
| C | UL89 hcmv terminase | protein | 221 | 41% helix, 26% strand | P16732 |
| D | UL89 hcmv terminase | protein | 214 | 43% helix, 26% strand | P16732 |
Ligands and binding sites
- C3W · 4-[(4-fluorophenyl)methyl-methyl-amino]-2,4-bis(oxidanylidene)butanoic acid · ligand · 4 copies · chains A, B, C, D
- MN · Manganese (II) ion · metal · 10 copies · chains A, B, C, D
- CL · Chloride ion · ion · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 467 | 0.64 | 0.77 | 42 | empty |
| 2 | 475 | 0.64 | 0.77 | 51 | empty |
| 3 | 148 | 0.47 | 0.77 | 25 | empty |
| 4 | 119 | 0.44 | 0.77 | 25 | empty |
| 5 | 104 | 0.44 | 0.78 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 881 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 876 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 547 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6EY7 · Human cytomegalovirus terminase nuclease domain, Mn soaked, inhibitor bound · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P16732
- Elsewhere: RCSB PDB 6EY7 · PDBe 6EY7 · UniProt P16732
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